Deciphering the core seed endo-bacteriome of the highland barley in Tibet plateau

Abstract

Highland barley (Hordeum vulgare var. nudum (L.) Hook.f., qingke) has unique physical and chemical properties and good potential for industrial applications. As the only crop that can be grown at high altitudes of 4200-4500 m, qingke is well adapted to extreme habitats at high altitudes. In this study, we analysed the seed bacterial community of 58 genotypes of qingke grown in different regions of Tibet, including qingke landraces, modern cultivars, and winter barley varieties, and characterised endophytic bacterial communities in seeds from different sources and the core endo-bacteriome of qingke. This study aim to provide a reference for the application of seed endophytes as biological inoculants for sustainable agricultural production and for considering microbe-plant interactions in breeding strategies. A total of 174 qingke seed samples from five main agricultural regions in Tibet were collected and subjected to investigation of endophytic endo-bacteriome using high-throughput sequencing and bioinformatics approaches. The phyla of endophytic bacteria in qingke seeds from different sources were similar; however, the relative proportions of each phylum were different. Different environmental conditions, growth strategies, and modern breeding processes have significantly changed the community structure of endophytic bacteria in seeds, among which the growth strategy has a greater impact on the diversity of endophytic bacteria in seeds. Seeds from different sources have conserved beneficial core endo-bacteriome. The core endo-bacteriome of qingke seeds dominated by Enterobacteriaceae may maintain qingke growth by promoting plant growth and assisting plants in resisting pests and diseases. This study reveals the core endo-bacteriome of qingke seeds and provides a basis for exploiting the endophytic endo-bacteriome of qingke seeds.

Keywords: core endo-bacteriome; endophytes; highland barley; qingke; seed.

Figure 1

Alpha diversity and beta diversity of endophytic bacterial communities in different types of qingke seeds. (A) Alpha diversity. The “*” represent significant difference among different types of qingke seeds at 0.05 level. (B) Beta diversity was evaluated by PCoA ranking based on Bray-Curtis distance. Different colored dots represent different types of qingke seeds. Using ANOSIM analysis to assess the significance of differences in endophytic bacterial community structure in different types of qingke seeds. Lh, Lhasa landrace; Lk, Shannan landrace; Ny, Nyingchi landrace; Qa, Qamdo landrace; Sh, Shigatse landrace; MC, modern cultivars; WB, winter barley.

Figure 2

Composition of endophytic bacteria in different types of qingke seeds. Only the top 5 most abundant phyla are displayed, and the less abundant phyla are summarized as “Others”.

Figure 3

Similarity of endophytic bacterial composition of different types of qingke seeds. (A) The composition of endophytic bacteria in qingke seeds. The phyla with abundances below 2% are summarized as “Others”. (B) The genus composition of different types of qingke seeds. Taxa with abundances below 1% are summarized as “Others” (C) Venn diagram of the seed phylum level of different types of qingke. (D) The genus level upset of different types of qingke seed genus.

Figure 4

Correlation network analysis at the genus level of endophytic bacteria in qingke seeds. The node colors represent different bacterial phyla, and the node size is proportional to the degree.

Figure 5

Using the Linear discriminant analysis Effect Size (LEfSe) method, the abundance of qingke seeds of different types of different bacterial taxa was revealed. (A) Clade diagram representation of the phylogenetic relationships of taxa with differences in abundance among qingke seeds from different sources. Nodes from inside to outside represent phyla, classes, orders, families, genera and species. (B) LEfSe analysis of endophytic bacteria in qingke seeds from different sources (P < 0.05, log LDA score threshold ≥ 3.3).